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Bacterial whole genome sequencing

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https://www.readbyqxmd.com/read/28819111/community-outbreaks-of-group-a-streptococcus-revealed-by-genome-sequencing
#1
Claire E Turner, Luke Bedford, Nicholas M Brown, Kim Judge, M Estée Török, Julian Parkhill, Sharon J Peacock
The frequent occurrence of disease outbreaks in humans caused by group A Streptococcus (GAS) is an on-going public health threat. Conventional bacterial typing methods lack the discriminatory power to confidently confirm or refute outbreaks in hospital and community settings. Microbial whole genome sequencing (WGS) provides a potential solution to this, but, there has been limited population-based surveillance with accompanying sequence data. We performed retrospective genomic surveillance of 93 clinical GAS isolates from individuals in a defined geographic region...
August 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28797043/next-generation-sequencing-reveals-the-antibiotic-resistant-variants-in-the-genome-of-pseudomonas-aeruginosa
#2
Babu Ramanathan, Hassan Mahmood Jindal, Cheng Foh Le, Ranganath Gudimella, Arif Anwar, Rozaimi Razali, Johan Poole-Johnson, Rishya Manikam, Shamala Devi Sekaran
Rapid progress in next generation sequencing and allied computational tools have aided in identification of single nucleotide variants in genomes of several organisms. In the present study, we have investigated single nucleotide polymorphism (SNP) in ten multi-antibiotic resistant Pseudomonas aeruginosa clinical isolates. All the draft genomes were submitted to Rapid Annotations using Subsystems Technology (RAST) web server and the predicted protein sequences were used for comparison. Non-synonymous single nucleotide polymorphism (nsSNP) found in the clinical isolates compared to the reference genome (PAO1), and the comparison of nsSNPs between antibiotic resistant and susceptible clinical isolates revealed insights into the genome variation...
2017: PloS One
https://www.readbyqxmd.com/read/28794988/whole-genome-sequencing-of-microbacterium-sp-aiso3-from-polluted-san-jacinto-river-sediment-reveals-high-bacterial-mobility-metabolic-versatility-and-heavy-metal-resistance
#3
Rupa Iyer, Ashish Damania, Brian Iken
The genus Microbacterium is composed of high GC content, Gram-positive bacteria of the phylum Acintobacteria known for their antibiotic production. Microbacterium species commonly colonize agricultural rhizospheres and more infrequently have been found to colonize and infect human tissues as well. Here we report the 3,696,310 bp draft genome (chromosome and plasmids) sequence assembled at the scaffold level from 232 contigs of Microbacterium sp. strain AISO3, isolated from polluted San Jacinto River sediment in Channelview, Texas...
December 2017: Genomics Data
https://www.readbyqxmd.com/read/28792800/national-antimicrobial-resistance-monitoring-system-two-decades-of-advancing-public-health-through-integrated-surveillance-of-antimicrobial-resistance
#4
Beth E Karp, Heather Tate, Jodie R Plumblee, Uday Dessai, Jean M Whichard, Eileen L Thacker, Kis Robertson Hale, Wanda Wilson, Cindy R Friedman, Patricia M Griffin, Patrick F McDermott
Drug-resistant bacterial infections pose a serious and growing public health threat globally. In this review, we describe the role of the National Antimicrobial Resistance Monitoring System (NARMS) in providing data that help address the resistance problem and show how such a program can have broad positive impacts on public health. NARMS was formed two decades ago to help assess the consequences to human health arising from the use of antimicrobial drugs in food animal production in the United States. A collaboration among the Centers for Disease Control and Prevention, the U...
August 9, 2017: Foodborne Pathogens and Disease
https://www.readbyqxmd.com/read/28790994/insight-into-the-origin-and-evolution-of-the-vibrio-parahaemolyticus-pandemic-strain
#5
REVIEW
Romilio T Espejo, Katherine García, Nicolas Plaza
A strain of Vibrio parahaemolyticus that emerged in 1995 caused the first known pandemic involving this species. This strain comprises clonal autochthonous ocean-dwelling bacteria whose evolution has occurred in the ocean environment. The low sequence diversity in this population enabled the discovery of information on its origin and evolution that has been hidden in bacterial clones that have evolved over a long period. Multilocus sequencing and microarray analysis, together with phylogenetic analysis, of pandemic and pre-pandemic isolates has suggested that the founder clone was an O3:K6 non-pathogenic strain that initially acquired a toxRS/new region and subsequently acquired at least seven novel genomic islands...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28782648/whole-genome-sequencing-of-campylobacter-jejuni-isolated-from-danish-routine-human-stool-samples-reveals-surprising-degree-of-clustering
#6
K G Joensen, K G Kuhn, L Müller, J T Björkman, M Torpdahl, J Engberg, H M Holt, H L Nielsen, A M Petersen, S Ethelberg, E M Nielsen
OBJECTIVES: Outbreaks of Campylobacter are traditionally considered to be rare, however rather than being the true nature of the disease, this may reflect our present inability to detect them. The aim of this study was to determine the genetic and epidemiological degree of clustering among Campylobacter jejuni isolates from Danish patients. METHODS: Whole-genome sequencing (WGS) was applied to 245 C. jejuni isolates from patients with domestically acquired infection over a 9-month period in 2015 and 2016...
August 3, 2017: Clinical Microbiology and Infection
https://www.readbyqxmd.com/read/28776118/thauera-phenolivorans-sp-nov-a-phenol-degrading-bacterium-isolated-from-activated-sludge
#7
Yajie Yin, Yanan Wang, Wei Tang, Liyan Song
A Gram-stain negative, short rod-shaped and non-motile bacterial strain ZV1C(T) capable of degrading phenol was isolated from a wastewater treatment system of Huafu mustard tuber salinity preservation factory in Chongqing, China. Aerobic growth was observed at 20-42 °C (optimum, 30 °C) and at pH 5-10 (optimum, pH 8). Cells tolerated NaCl concentrations of 0-2% (w/v) (optimum, 0%). The major respiratory quinone is ubiquinone Q-8 and the major cellular fatty acids are C16:1 ω7c /C16:1 ω6c and C16:0. The 16S rRNA gene sequence of stain ZV1C(T) is phylogenetically related to the 16S rRNA genes of the type strains of Thauera species (similarity: 96...
August 3, 2017: Antonie Van Leeuwenhoek
https://www.readbyqxmd.com/read/28771118/marinomonas-epiphytica-sp-nov-isolated-from-a-marine-intertidal-macroalga
#8
Anup Kumar Ojha, Ashish Verma, Yash Pal, Deepak Bhatt, Shanmugam Mayilraj, Srinivasan Krishnamurthi
A novel Gram-stain-negative, aerobic marine bacterial strain, SAB-3T, was isolated from brown macroalgae (Dictyota sp.) growing in the Arabian sea, Goa, India. The strain grew optimally at 30 °C, with 2.0-4.0 % (w/v) NaCl and at pH 7.0 on marine agar medium. Strain SAB-3T was unable to hydrolyse aesculin and did not grow in the presence of rifamycin but showed resistance to antibiotics such as cefadroxil and co-trimoxazole. The major fatty acids were summed feature 8 (C18 : 1ω7c/C18 : 1ω6c), summed feature 3 (C16 : 1ω7c/C16 : 1ω6c) and C16 : 0, and Q-8 was the major ubiquinone...
August 4, 2017: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/28768482/comparative-genomic-analysis-and-characterization-of-incompatibility-group-fib-plasmid-encoded-virulence-factors-of-salmonella-enterica-isolated-from-food-sources
#9
Bijay K Khajanchi, Nur A Hasan, Seon Young Choi, Jing Han, Shaohua Zhao, Rita R Colwell, Carl E Cerniglia, Steven L Foley
BACKGROUND: The degree to which the chromosomal mediated iron acquisition system contributes to virulence of many bacterial pathogens is well defined. However, the functional roles of plasmid encoded iron acquisition systems, specifically Sit and aerobactin, have yet to be determined for Salmonella spp. In a recent study, Salmonella enterica strains isolated from different food sources were sequenced on the Illumina MiSeq platform and found to harbor the incompatibility group (Inc) FIB plasmid...
August 2, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28757017/characterization-of-ndm-5-positive-extensively-resistant-escherichia-coli-isolates-from-dairy-cows
#10
Tao He, Ruicheng Wei, Lili Zhang, Lichang Sun, Maoda Pang, Ran Wang, Yang Wang
The aim of this study was to investigate the prevalence of blaNDM-5 gene in Escherichia coli isolates from dairy cows and to characterize the molecular traits of the blaNDM-5-positive isolates. A total of 169 cows were sampled (169 feces and 169 raw milk samples) in three dairy farms in Jiangsu Province and 203 E. coli isolates were recovered. Among these strains, three isolates carried blaNDM-5 gene, including one co-harboring mcr-1, which belonged to sequence type 446 and the other two belonged to ST2. Susceptibility testing revealed that the three blaNDM-5-positive isolates showed extensive resistance to antimicrobials...
August 2017: Veterinary Microbiology
https://www.readbyqxmd.com/read/28753663/metasnv-a-tool-for-metagenomic-strain-level-analysis
#11
Paul Igor Costea, Robin Munch, Luis Pedro Coelho, Lucas Paoli, Shinichi Sunagawa, Peer Bork
We present metaSNV, a tool for single nucleotide variant (SNV) analysis in metagenomic samples, capable of comparing populations of thousands of bacterial and archaeal species. The tool uses as input nucleotide sequence alignments to reference genomes in standard SAM/BAM format, performs SNV calling for individual samples and across the whole data set, and generates various statistics for individual species including allele frequencies and nucleotide diversity per sample as well as distances and fixation indices across samples...
2017: PloS One
https://www.readbyqxmd.com/read/28750049/genome-target-evaluator-gtevaluator-a-workflow-exploiting-genome-dataset-to-measure-the-sensitivity-and-specificity-of-genetic-markers
#12
Arnaud Felten, Laurent Guillier, Nicolas Radomski, Michel-Yves Mistou, Renaud Lailler, Sabrina Cadel-Six
Most of the bacterial typing methods used to discriminate isolates in medical or food safety microbiology are based on genetic markers used as targets in PCR or hybridization experiments. These DNA typing methods are important tools for studying prevalence and epidemiology, for conducting surveillance, investigations and control of biological hazard sources. In that perspective, it is crucial to insure that the chosen genetic markers have the greatest specificity and sensitivity. The wealth of whole-genome sequences available for many bacterial species offers the opportunity to evaluate the performance of these genetic markers...
2017: PloS One
https://www.readbyqxmd.com/read/28741995/merdimonas-faecis-gen-nov-sp-nov-isolated-from-human-faeces
#13
Boram Seo, Ju Eun Yoo, Yung Mi Lee, GwangPyo Ko
A strictly anaerobic Gram-stain-positive, non-motile and non-spore-forming bacterial strain, BR31T, was isolated from a faecal sample of a healthy human. Bacterial colonies were ivory-coloured on GAM agar and composed of rod-shaped cells with rounded ends approximately 1.4-2.1×0.5-0.6 µm in size. According to comparative analysis based on 16S rRNA gene sequences, strain BR31T formed a distinct phylogenetic lineage that reflects a new genus within Clostridium cluster XIVa in the family Lachnospiraceae, with highest similarity to Eubacterium contortum DSM 3982T (94...
July 26, 2017: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/28740489/prophage-integrase-typing-is-a-useful-indicator-of-genomic-diversity-in-salmonella-enterica
#14
Anna Colavecchio, Yasmin D'Souza, Elizabeth Tompkins, Julie Jeukens, Luca Freschi, Jean-Guillaume Emond-Rheault, Irena Kukavica-Ibrulj, Brian Boyle, Sadjia Bekal, Sandeep Tamber, Roger C Levesque, Lawrence D Goodridge
Salmonella enterica is a bacterial species that is a major cause of illness in humans and food-producing animals. S. enterica exhibits considerable inter-serovar diversity, as evidenced by the large number of host adapted serovars that have been identified. The development of methods to assess genome diversity in S. enterica will help to further define the limits of diversity in this foodborne pathogen. Thus, we evaluated a PCR assay, which targets prophage integrase genes, as a rapid method to investigate S...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28739600/whole-genome-sequencing-and-concordance-between-antimicrobial-susceptibility-genotypes-and-phenotypes-of-bacterial-isolates-associated-with-bovine-respiratory-disease
#15
Joseph R Owen, Noelle Noyes, Amy E Young, Daniel J Prince, Patricia C Blanchard, Terry W Lehenbauer, Sharif S Aly, Jessica H Davis, Sean M O'Rourke, Zaid Abdo, Keith Belk, Michael R Miller, Paul Morley, Alison Van Eenennaam
Extended laboratory culture and antimicrobial susceptibility testing timelines hinder rapid species identification and susceptibility profiling of bacterial pathogens associated with bovine respiratory disease, the most prevalent cause of cattle mortality in the United States. Whole genome sequencing offers a culture-independent alternative to current bacterial identification methods but requires a library of bacterial reference genomes for comparison. To contribute new bacterial genome assemblies and evaluate genetic diversity and variation in antimicrobial resistance genotypes, whole-genome sequencing was performed on bovine respiratory disease associated bacterial isolates (Histophilus somni, Mycoplasma bovis, Mannheimia haemolytica, and Pasteurella multocida) from dairy and beef cattle...
July 24, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28732529/exiguobacterium-sp-a1b-gx59-isolated-from-a-patient-with-community-acquired-pneumonia-and-bacteremia-genomic-characterization-and-literature-review
#16
Xingchun Chen, Lijun Wang, Jiali Zhou, Honglong Wu, Dong Li, Yanchao Cui, Binghuai Lu
BACKGROUND: Bacterial species belonging to the genus Exiguobacterium are facultative anaerobic, non-spore-forming, Gram-positive bacilli, and rarely associated with human infections. Herein, we reported the first case of community-acquired pneumonia (CAP) and bacteremia due to Exiguobacterium spp. in China. CASE PRESENTATION: An adult male with severe CAP was hospitalized. The pathogen was isolated from his bloodstream and broncho-alveolar lavage fluid. The correct identification of the micro-organism was achieved using 16S rRNA sequencing, and its antibiotic susceptibility test was performed by microdilution method...
July 21, 2017: BMC Infectious Diseases
https://www.readbyqxmd.com/read/28724393/methicillin-resistant-staphylococcus-aureus-emerged-long-before-the-introduction-of-methicillin-into-clinical-practice
#17
Catriona P Harkins, Bruno Pichon, Michel Doumith, Julian Parkhill, Henrik Westh, Alexander Tomasz, Herminia de Lencastre, Stephen D Bentley, Angela M Kearns, Matthew T G Holden
BACKGROUND: The spread of drug-resistant bacterial pathogens poses a major threat to global health. It is widely recognised that the widespread use of antibiotics has generated selective pressures that have driven the emergence of resistant strains. Methicillin-resistant Staphylococcus aureus (MRSA) was first observed in 1960, less than one year after the introduction of this second generation beta-lactam antibiotic into clinical practice. Epidemiological evidence has always suggested that resistance arose around this period, when the mecA gene encoding methicillin resistance carried on an SCCmec element, was horizontally transferred to an intrinsically sensitive strain of S...
July 20, 2017: Genome Biology
https://www.readbyqxmd.com/read/28720731/an-in-vitro-chicken-gut-model-demonstrates-transfer-of-a-multidrug-resistance-plasmid-from-salmonella-to-commensal-escherichia-coli
#18
Roderick M Card, Shaun A Cawthraw, Javier Nunez-Garcia, Richard J Ellis, Gemma Kay, Mark J Pallen, Martin J Woodward, Muna F Anjum
The chicken gastrointestinal tract is richly populated by commensal bacteria that fulfill various beneficial roles for the host, including helping to resist colonization by pathogens. It can also facilitate the conjugative transfer of multidrug resistance (MDR) plasmids between commensal and pathogenic bacteria which is a significant public and animal health concern as it may affect our ability to treat bacterial infections. We used an in vitro chemostat system to approximate the chicken cecal microbiota, simulate colonization by an MDR Salmonella pathogen, and examine the dynamics of transfer of its MDR plasmid harboring several genes, including the extended-spectrum beta-lactamase blaCTX-M1 We also evaluated the impact of cefotaxime administration on plasmid transfer and microbial diversity...
July 18, 2017: MBio
https://www.readbyqxmd.com/read/28713356/a-genotypic-analysis-of-five-p-aeruginosa-strains-after-biofilm-infection-by-phages-targeting-different-cell-surface-receptors
#19
Diana P Pires, Andreas Dötsch, Erin M Anderson, Youai Hao, Cezar M Khursigara, Joseph S Lam, Sanna Sillankorva, Joana Azeredo
Antibiotic resistance constitutes one of the most serious threats to the global public health and urgently requires new and effective solutions. Bacteriophages are bacterial viruses increasingly recognized as being good alternatives to traditional antibiotic therapies. In this study, the efficacy of phages, targeting different cell receptors, against Pseudomonas aeruginosa PAO1 biofilm and planktonic cell cultures was evaluated over the course of 48 h. Although significant reductions in the number of viable cells were achieved for both cases, the high level of adaptability of the bacteria in response to the selective pressure caused by phage treatment resulted in the emergence of phage-resistant variants...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28711508/virulent-and-pathogenic-features-on-the-cronobacter-sakazakii-polymyxin-resistant-pmr-mutant-strain-s-3
#20
Xuerui Bao, Ling Yang, Lequn Chen, Bing Li, Lin Li, Yanyan Li, Zhenbo Xu
Cronobacter sakazakii is a well-known opportunistic pathogen responsible for necrotizing enterocolitis, meningitis and septicaemia in the premature, immunocompromised infants and neonates. This pathogen possesses various virulence factors and regulatory systems, and pmrA/pmrB regulatory system has been identified in a variety of bacterial species. The current study aims to investigate role of pmrA gene in the pathogenicity and virulence characteristics of Cronobacter sakazakii using whole genome sequencing and RNA-seq...
July 12, 2017: Microbial Pathogenesis
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